Welcome to Seabed Habitats


Welcome to Seabed Habitats- The newest blog about everything to do with marine habitats.The marine realm is such a dynamic system and is very much an “unexplored wilderness.” Being a relatively new science (with most sub-disciplines being only 50-120 years old), a lot of work is being done to gain a thorough understanding. With technological advances happening rapidly, there are always new methods to try out and new equipment to test. With research being so interdisciplinary in nature, spanning a range of areas such as marine ecology, marine geology, coastal processes, geophysics, oceanography, hydrography, remote sensing, surveying, GIS.. This blog attempts to keep you up to date on the latest developments in the field. From new research ideas to images to the latest technology- all can be discussed here.

Porosity- the Philosophy of Life



A philosophy professor stood before his class with items on the table in front of him. When the class began, he picked up a very large and empty jar and proceeded to fill it with rocks. He then asked the students if the jar was full. They agreed that it was.

So the professor then picked up some pebbles and poured them into the jar. He shook the jar lightly. The pebbles of course rolled in to the open areas between the rocks. He then asked the students again if the jar was full. They agreed it was.

The professor picked up some sand and poured it into the jar. Of course, the sand filled up everything else. He then asked once more if the jar was full. The students responded with a unanimous “yes.”

The professor then produced two cans of beer from under the table and proceeded to pour their entire contents into the jar- effectively filling the empty space between the sand. The students laughed. “Now,” said the professor as the laughter subsided, “I want you to recognise that this jar represents your life. The rocks are the important things; Your life, Your health, Your family, things that if everything else was lost and only they remained, your life would still be full. The pebbles are the other things that matter- like your job, your home, your career. The sand is everything else- the small stuff which seems important but is not really that necessary. If you put the sand into the jar first, there is no room for the pebbles or the rocks. The same goes for your life. If you spend all your time on the small stuff, you will never have room for the things that are important to you. Pay attention to things that are critical to your happiness. But if you put the rocks in first; the things that really matter in your life, than your life will be a lot more fulfilling and happier. Set your priorities; the rest is just sand.”

One of the students raised their hand and enquired what the beer represented? The professor smiled, “I am glad you asked. It goes to show, no matter how full your life may seem, there is always room for a couple of beers.”

(Author unknown)

Porosity: The science

Porosity (p) in sediment dynamics is the ratio of the volume of voids, to the total volume. For non-cohesive sediments such as sand, p= 0.3 to 0.4. Well-graded and poorly sorted sediments have a large standard deviation of the mean, with p= 0.3. Poorly graded and well sorted sediments have a small standard deviation of the mean with large porosity, with p=0.4. Coastal engineers often take p=0.35 when the actual value is unknown.

This is a story I heard from David Basco, Old Dominion University, Virginia, USA, during his lectures in Coastal Hydrodynamics and Sediment Transport. In Plymouth, I had the opportunity to meet him and his wife in person, and share with him this photograph of our outreach activity at the National University of Ireland, Galway, a jar full of oranges, marbles and maerl.

Michael and the Peppermints


This year at the Beneath the Waves Film Festival, the 2014 People’s Choice award went to “Michael and the Peppermints” created by Michael and Chelsey Crandall starring Michael Dickson. Ocypode Productions presents a profile of University of Florida Graduate Student Michael Dickson. This short documentary takes a look at Michael’s work, both in the field and in the lab, as he conducts scientific research into the ecology and population structure of peppermint shrimp in the Gulf of Mexico. A poster of the Beneath the Waves film festival can be found at the artist’s following  link. The team also have a new paper out discussing the impact of film-making and film festivals in disseminating scientific research, complimenting scientific meetings. Their mission is to:

The mission of Beneath the Waves, Inc. and the Beneath the Waves Film Festival is to raise public awareness with regards to ocean conservation and marine science through the use of visual and digital media such as videos. We also seek to promote science communication and scientific literacy by encouraging and inspiring scientists, ocean enthusiasts, and members of the general public to produce, promote and communicate research and conservation through open-access, engaging short films.

Beneath the Waves


Staaterman et. al. 2014, Lights, camera, science: The utility and growing popularity of film festivals at scientific meetings, Ideas in Ecology and Evolution, Volume 7 Number 1.

The Beneath the Waves Film Festival website

Virtual Dive in Emily’s Pinnacles, Bermuda


Emily’s Pinnacles are impressive hard coral formations found in Bermuda and provide the building blocks for the reef. Darwin classified three main types of reefs – barrier reefs, fringing reefs and atolls, with others being patch reef and pinnacle reefs. A pinnacle reef occur when a patch reef occurs at an open shelf, rather than at an atoll.

Here, Google have partnered with The Catlin Seaview Survey, a major scientific study of the world’s reefs, to make these amazing images available to millions of people through the Street View feature of Google Maps. The Catlin Seaview Survey used a specially designed underwater camera, the SVII, to capture these photos.  For further views please see the Google Street view Ocean gallery. For more information about the Catlin Seaview Survey please view their website. Explore it here, with brain corals below:

Brain coral is a common name given to corals in the family Faviidae so called due to their generally spheroid shape and grooved surface which resembles a brain. Each head of coral is formed by a colony of genetically identical polyps which secrete a hard skeleton of calcium carbonate; this makes them important coral reef builders like other stony corals in the order Scleractinia. The corals reefs of Bermuda have been especially vulnerable to coral bleaching. Bleaching occurs when the conditions necessary to sustain the coral’s zooxanthellae cannot be maintained and is a generalized stress response of corals.


Morelock J, 2005, Reef Types, Personal Webpage

More on pinnacle reef formation near patch reefs and mounds can be found here: SEPM Strata: Carbonate Facies

Wikipedia- “Brain Coral” and “Coral Bleaching

Multibeam Backscatter vs. Sidescan Sonar Imagery


Multibeam backscatter is the reflectivity measurement, where as the sidescan sonar imagery is the actual intensity of the return signal. The Sidescan sonar towing configuration provides greater maneuverability, as the depth of the tow-fish above the seafloor can be adjusted, in view of the swath width. For example, the sidescan imagery is less prone to be affected by the slope of the seafloor as it can be positioned, where as the multibeam can only receive the backscatter intensity as it reaches the survey vessel.

The footprint size at the outer beam of the sidescan sonar is larger than at the nadir beam as slant range is greater in the far range; subsequently increasing the two way travel time of the acoustic signal. A larger footprint has a greater uncertainty of detecting the first return, as well as a lower resolution. Hence, the theoretical maximum speed at which the survey vessel should go can be calculated, to ensure not only 100% coverage of the along track beam footprint, but also optimize the footprint size for all the beams. Therefore speed is an important factor to consider when planning a survey.

Thus practically, gaps in the multibeam data sets are present if the survey speed is too fast, as the vessel would have moved away before the acoustic return can reach the receiver. On the other hand, multibeam surveying uses expensive resources, such as ship fuel and a very slow survey speed would use the resources with a limited efficiency, resulting in a smaller area ensonified in the survey. Additional effects are also present for the sidescan sonar as the system comprises of a towed fish. Slow speeds may result in the fish having a decreased momentum/tension in the cable, changing the position of the fish relative to the vessel.

The difference between multibeam positioning and the sidescan sonar positioning is that the sidescan towed fish is found behind the ship, and hence this needs to be corrected for, in relation to the on board DGPS navigation system. This can be done most simply by doing trigonometric calculations, based on the length of the cable out (lay back) and the depth of the fish above the seafloor, as well as accounting for the heading. Base line acoustic positioning systems may also be used, with an acoustic signal being sent by the fish to the vessel, or by triangulation with transducers being based on the seafloor. Similarly the position of the multibeam transducer and receiver on the vessel also needs to be added to a vessel configuration file during processing. Furthermore, a time-lag correction needs to be applied, ensuring the correct position is recorded, with synchronized times of the navigation and the satellite.

If a survey was taken at another time of the year then different weather conditions affecting the movement of the survey vessel in the x,y and z directions would be recorded in the raw data acquired. Hence, attitude sensors on the vessel need to be used to correct the data to different types of movement, or the roll, pitch, heave and yaw. The pitch is a measure of the rotation of the survey vessel in the x axis; the roll is the rotation in the y axis and heave in the z axis. The yaw is the offset between the survey lines. A consequence of more turbulent weather conditions, which has a greater impact on the sidescan system, is the increased presence of air bubbles. This affects the way sound propagates in the surface mixed layer and hence can cause artefacts in the data. Bubbles may also originate from the propellers of other vessels which may be present at other times of survey.

The sea floor composition and the angle of incidence primarily cause variation in backscatter intensity, according to Lambert’s law. The roughness and hardness or acoustic impedance of the sea floor are two key parameters which vary with geological and biological characteristics. These parameters have varying contributions to the backscatter intensity, depending on the angle of incidence. Hence the energy of the ping which is reflected or absorbed is affected by the sediment geotechnical properties, as well as by the grazing angle. Additionally, scattering by targets (e.g. fish, zooplankton, submarines) in the water column can alter the backscatter intensity. Other factors to consider affecting the strength of the backscatter are the depth of the water column and the initial energy of the acoustic signal, as transmission loss occurs in the water column. Here is an example of multibeam backscatter acquired using Reson 7125 system.